Package: SiPhyNetwork 1.1.0

Joshua Justison

SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution

A simulator for reticulate evolution under a birth-death-hybridization process. Here the birth-death process is extended to consider reticulate Evolution by allowing hybridization events to occur. The general purpose simulator allows the modeling of three different reticulate patterns: lineage generative hybridization, lineage neutral hybridization, and lineage degenerative hybridization. Users can also specify hybridization events to be dependent on a trait value or genetic distance. We also extend some phylogenetic tree utility and plotting functions for networks. We allow two different stopping conditions: simulated to a fixed time or number of taxa. When simulating to a fixed number of taxa, the user can simulate under the Generalized Sampling Approach that properly simulates phylogenies when assuming a uniform prior on the root age.

Authors:Joshua Justison [aut, cre, cph], Claudia Solis-Lemus [aut, cph], Tracy A. Heath [aut, cph], Klaus Schliep [cph], Emmanuel Paradis [cph], Daniel Lawson [cph]

SiPhyNetwork_1.1.0.tar.gz
SiPhyNetwork_1.1.0.tar.gz(r-4.5-noble)SiPhyNetwork_1.1.0.tar.gz(r-4.4-noble)
SiPhyNetwork_1.1.0.tgz(r-4.4-emscripten)SiPhyNetwork_1.1.0.tgz(r-4.3-emscripten)
SiPhyNetwork.pdf |SiPhyNetwork.html✨
SiPhyNetwork/json (API)
NEWS

# Install 'SiPhyNetwork' in R:

install.packages('SiPhyNetwork', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

25 exports 0.00 score 10 dependencies 17 scripts 1.1k downloads

Last updated 1 years agofrom:2f0bf319ff. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 25 2024
R-4.5-linux-x86_64	NOTE	Aug 25 2024

Exports:biconnectedComponents deleteTips getNetworkLevel incompleteSampling isFUstable isNormal isTreeBased isTreeChild ltt.network make.beta.draw make.categorical.draw make.exp.decay make.linear.decay make.polynomial.decay make.stepwise make.trait.model make.uniform.draw network.gsa plottable.net read.net reconstructedNetwork sim.bdh.age sim.bdh.taxa.gsa sim.bdh.taxa.ssa write.net

Dependencies:ape cli digest glue lattice lifecycle nlme Rcpp rlang rstackdeque

Introduction

Josh Justison

Rendered fromintroduction.Rmdusingknitr::knitron Aug 25 2024.

Last update: 2023-04-14
Started: 2022-09-20

Help page	Topics
Biconnected Components	biconnectedComponents
Remove tips from a phylogenetic Network	deleteTips
Get the level of a Network	getNetworkLevel
Sample Tips on a Phylogenetic Network	incompleteSampling
Determine whether a phylogeny is FU-stable	isFUstable
#' Determine whether a phylogeny is Normal	isNormal
Determine whether a network is tree-based	isTreeBased
Determine whether a network is tree-child	isTreeChild
Lineages thru time on a network	ltt.network
Function that makes a draw from a beta distribution	make.beta.draw
Function that makes a draw from a categorical distribution	make.categorical.draw
Make an exponential decay function	make.exp.decay
Make a linear decay function	make.linear.decay
Make a polynomial decay function	make.polynomial.decay
Make a stepwise decay function	make.stepwise
Model for trait evolution across the phylogeny	make.trait.model
Function that makes a draw from a uniform distribution	make.uniform.draw
Sample under the Generalized Sampling Approach	network.gsa
Create a more Plotting-Friendly phylogenetic Network	plottable.net
Read a Network from Parenthetic Format	read.net
Remove Extinct Lineages from a Phylogenetic Network	reconstructedNetwork
Simulate a Phylogenetic Network to a Specified Number of Taxa	sim.bdh.age
Simulate a Phylogenetic Network to a Specified Number of Taxa	sim.bdh.taxa.gsa
Simulate a Phylogenetic Network to a Specified Number of Taxa	sim.bdh.taxa.ssa
Write a Network in Parenthetic Format	write.net

Package: SiPhyNetwork 1.1.0

SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution

Introduction

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)